Book of Germs: The Quest for a Field Guide to Microbes

Every nature lover knows field guides, those handy compendia of the natural world. There are thousands of titles for birds alone, but microbes have been largely overlooked, even though their total biomass is equivalent to all the plants and animals on Earth. And the field guides that do exist are far from comprehensive.

Evolutionary biologist Jonathan Eisen wants to change that.

"As a little kid, I carried around my binoculars and wanted to check off everything on my list," said Eisen, whose youthful hobby would lead to professional research on hummingbirds and butterflies, which was followed by his current focus on bacteria. "That’s how I was inspired to do a microbial field guide."

Eisen, whose laboratory is located in the University of California, Davis, Genome Center, proposed building a field guide for microbes at the recent American Association for the Advancement of Science's annual conference in Vancouver. He wants it to be a collaboration between experts and citizen scientists, like other field guides are.

The guide wouldn't just be a static book. Eisen, a field guide junky, has dozens of those, but he's also enthralled by iBird, an iPhone app replete with pictures and songs and spotting tips. "I dream of having the equivalent for microbes," he said during his talk.

Wired asked Eisen about his proposal.

Wired: What information would you include?

Jonathan Eisen: Just like bird field guides have raptors, sparrows and crows, this would have the major lineages and taxonomic subgroups, all the way down to species.

The second part would be ranges: the distribution patterns of microbes across the planet. Then there would be some text or visual description of niches where you’d find the organism.

Then it would have some description of the organism's biology. That would typically include appearance and behavior, but microbes don’t have a lot of things we would call behaviors -- so instead you’d have biochemistry and physiology. Does it make hydrogen? Does it convert carbon into sugar? You can imagine descriptions of their biology: Some might be predators. Some might be herbivores. Some might be everything in between.

A really important thing for field guides, in particular for the actual field, is the means to identify. For microbes that’s probably going to involve genetic signatures. It would also be really cool to have a checklist, which is a really popular part of other field guides. When you see something, you check it off your list and then you move on. It gives encouragement to go out and find things.

Images: 1) French postcard (c. 1900) depicting how scientists would look at microbes in the year 2000. Wikimedia Commons. 2) Jonathan Eisen displays his iBird field guide on his iPhone. (Jonathan Eisen)

Wired: What are the advantages of having a microbe field guide?

Eisen: The number-one advantage is as a concept to drive the gathering of information. Field guides help people know what they need to gather about organisms. If you see that for 10 organisms you don’t have a range map, that tells you, “I should really fill in the ranges.”

Once you have a working field guide, you can interpret changes. People use bird field guides to study global climate change. By having amateurs and professionals out there comparing modern patterns to their field guides, they can tell if something has changed. This is another thing I love about the field guide concept: It’s taking something that's in the ivory tower and giving it to everyone.

Wired: What is the biggest obstacle to having a field guide for microbes?

Eisen: Diversity. There are probably different microbes if you move two millimeters in a pile of soil. The diversity is bigger than galaxies in the universe. But this hasn’t stopped the Galaxy Zoo people from trying to classify galaxies.

Wired: Couldn't you just have separate field guides for separate microbes?

Eisen: Yes, alternatively you could have a separate field guide to each group, just like people do for different animals, but it just doesn’t carry the same ring to it. Right now people don’t say I’m really interested in the chlamydias! So we have to do them all at once for now.

Image: A 20-cm-wide xenophyophore, a type of seafloor-dwelling protist. In some locations, such as the bottom of deep-sea trenches, they may reach population densities of 2,000 per 100 square meters. NOAA / Wikimedia Commons.

Wired: To develop and use the guide, would we need new technologies for mobile devices and smartphones?

Eisen:There's no doubt there will be portable DNA testing devices. Oxford Nanopore Technologies announced a DNA sequencer in a thumb drive. They didn’t share data, so some people still aren't certain it works, but you plug it into your computer and then add some DNA sample to the other end. It does the sequencing and dumps the data into your computer. According to the company, you can do this now.

In a couple of years people will be able to walk around and sample their soil. People could go to their backyards. We could get every high school biology class in the country to collect pond water samples. We would have a map like nobody has ever had before.

Image: These jelly balls are colonies of the cyanobacteria species Nostoc pruniforme("Mare's eggs"), which live in freshwater ponds. Wikipedia.

Wired: How would the field guide work?

We need to have visualization and data processing tools that make useful representations. You could have a heat map of biodiversity, then zoom in on the species you’re interested in, like with Google Maps street view.

Wired: How do you engage people in studying microbes when they're often equated with pathogens?

Eisen: There are microbes that kill people. So I don’t want to portray all microbes on the planet as good. To educate people about microbes, I think we need to captivate people in some way.

The most obvious is the microbes in and on people. I could imagine engaging people in thinking about the diversity of microbes within a human body: the field guide to the human body. That's one way to get people to think about how not all microbes are bad. Another way to do this is to pick a non-human environment like ponds and develop a game or a high school science competition.

Eisen: We had a citizen microbiology workshop at UC Davis. People sampled microbes in their hot water heaters. Your hot water heater is cooking things on and off, and what survives that is really interesting.

We invited a birder to the workshop. He doesn’t do anything with microbes, but he does citizen birding. He had a great idea to sample microbes on bird feeders.

There's another one where people are sampling aquariums, a brilliant idea by Josh Neufeld. People are obsessed with their aquariums. They go to conferences, they blog about it, they monitor their fish. Obviously they’re going to be interested in microbes because they care about nitrogen metabolism and the oxygen in their tanks. He's getting lots of samples from people.

Eisen: I love engaging people in the entire process. The aquarium sampling is really interesting because people are doing experiments on their aquariums to see how they can change oxygen levels to get rid of parasites. They’re scientists. They may not call themselves that, but they are. A lot of the birders are too.

People will be interested. People love biology. They love the world around them. That’s why people are really into birds, butterflies and horticulture. Microbes are invisible. People are not going to be engaged until there’s some way they can get the data. But that’s possible now.

Wired: What are the larger implications of people using a microbial field guide to conduct science?

Eisen: The future of personalized medicine is people gathering lots of data about themselves. That can inform health decisions. Whether or not the medical community or the FDA want people to do it, they’re going to. We need to figure out how to deal with this, how to educate people about microbes, and that’s one of the reasons to do these citizen science projects.

Whether it’s about the human microbiome or microbes in water, we can educate people about microbial diversity, and that’s going to be important when they start sampling themselves.

Data’s going to be used in many other places, too. People will collect data about water quality and about the air. Home brewing, anything that involves fermentation, will also be affected. Farmers will collect data about their soil. On a global level, agriculture will be one of the biggest things impacted by studying microbes.

Local climate information could be impacted, too. Lots of people gather information about ocean currents and temperature and snow levels. Yet we’re missing information about some of the main players in the fixation of carbon and the production of carbon: the microbes that make much of it happen.

Eisen: People have suggested parts of it before. It’s amazing that it’s finally feasible to do it. I wouldn't have thought this possible even three or four years ago. The technology has gone completely crazy. It’s like experiencing a logarithmic curve. Every year things get so much cheaper and so much easier. Now, we’re just limited in part by imagination. By having this map, by having this field guide, we'll be able to do more experiments to figure out what microbes are doing in the planet.

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